Using R and bioconductor.
I'm not sure how to understand an integer rle that you'd get from functions like coverage() such as this
integer-Rle of length 3312 with 246 runs
Lengths: 25 34 249 16 7 11 16 ... 2 32 2 26 34 49
Values : 0 1 0 1 2 3 2 ... 1 2 1 0 1 0
Probably it's better to ask about Bioconductor packages on the Bioconductor support site.
The interpretation is that there is a run of 25 nucleotides with 0 coverage, then a run of 24 nucleotides with 1 coverage (i.e., a single read) then another run of 249 nucleotides with no coverage, then things start to get interesting as multiple reads overlap positions. From the summary line at the top of the output, your read covers 3312 nucleotides, maybe from a single transcript? If you were to
you'd get a quick plot of how coverage varies along the length of the transcript.
sum(coverage) is appropriate; a more usual metric is to count reads rather than coverage, e.g., with
GenomicRanges::summarizeOverlaps() illustrated in this DESeq2 work flow in the context of RNA-seq.